iSeq (version 1.24.0)

plotreg: A function used to plot enriched genomic regions

Description

A function used to plot enriched genomic regions.

Usage

plotreg(gpos,ipct,conct,peak,col=c("yellow","green","grey0","blue"))

Arguments

gpos

A n by 2 matrix or data frame. The rows correspond to genomic bins. The first and second columns contain the start and end positions of the genomic windows/bins, respectively.

ipct

A n by 2 matrix containing the ChIP tag counts corresponding to the bins in gpos. ipct[,1] contains the counts for the chain 1 (usually the forward chain); ipct[,2] contains the counts for the chain 2 (usually the reverse chain).

conct

A n by 2 matrix containing the control tag counts corresponding to the bins in gpos. ipct[,1] contains the counts for the chain 1 (usually the forward chain); ipct[,2] contains the counts for the chain 2 (usually the reverse chain).

peak

A vector containing the peak (center) positions of the genomic regions.

col

The colors used to fill the rectangles. col[1] is used for ipct[,1], col[2] for ipct[,2], col[3] for conct[,1] and col[4] for conct[,2], respectively.

Value

No value returned.

References

Qianxing Mo. (2012). A fully Bayesian hidden Ising model for ChIP-seq data analysis. Biostatistics 13(1), 113-28.

See Also

iSeq1, iSeq2, peakreg,mergetag

Examples

#see the example in iSeq1